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SlivkaWSDiscoverer formatting fix
[jalview.git]
/
src
/
jalview
/
analysis
/
2019-08-13
Jim Procter
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into...
tree
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commitdiff
2019-08-09
gmungoc
JAL-3187 removal of variant feature (non-virtual) trans...
tree
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commitdiff
2019-07-15
Jim Procter
Merge branch 'merge/JAL-3285_mchmmer_with_211_develop...
tree
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commitdiff
2019-07-12
Thomas
JAL-2629 add sort by evalue and bit score
tree
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commitdiff
2019-07-10
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-07-10
Jim Procter
Merge branch 'merge/JAL-3285_mchmmer_with_211_develop...
tree
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commitdiff
2019-07-03
tva
JAL-2629 evalues and bit scores now conserved after...
tree
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commitdiff
2019-06-18
gmungoc
JAL-3313 don't double count mapped codons
tree
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commitdiff
2019-06-17
gmungoc
JAL-3187 update alignAs code and unit tests for 'shared...
tree
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commitdiff
2019-06-11
gmungoc
JAL-3187 CDS has same dataset sequence as transcript
tree
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commitdiff
2019-06-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
tree
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commitdiff
2019-06-06
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-06-05
tva
JAL-3285 change method declaration in AAFrequency to...
tree
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commitdiff
2019-06-04
Jim Procter
Merge branch 'develop' into developtomchmmer
tree
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commitdiff
2019-04-11
Jim Procter
Merge branch 'develop' into task/JAL-3130_Java_11_inves...
tree
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commitdiff
2019-03-27
gmungoc
JAL-2620 improved error reporting on failure to load...
tree
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commitdiff
2019-03-21
Ben Soares
JAL-3130 Replaced deprecated Class.newInstance() with...
tree
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commitdiff
2019-03-20
Ben Soares
JAL-3130 Lots of deprecation fixes. See utils/deprecat...
tree
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commitdiff
2019-03-11
gmungoc
JAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test...
tree
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commitdiff
2019-03-07
gmungoc
Merge branch 'feature/JAL-3205symmetricCalc' into develop
tree
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commitdiff
2019-03-05
gmungoc
Merge remote-tracking branch 'origin/features/JAL-2620a...
tree
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commitdiff
2019-03-05
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-2839findWi...
tree
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commitdiff
2019-03-03
gmungoc
JAL-3205 faster calculation with symmetric score matrix
tree
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commitdiff
2019-02-28
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into merge...
tree
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commitdiff
2019-02-20
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into feature...
tree
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commitdiff
2019-02-19
gmungoc
JAL-3187 hacks to get peptide variant in to Jmol hover...
tree
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commitdiff
2019-01-21
gmungoc
JAL-3187 (hacked up) show complement features on struct...
tree
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commitdiff
2019-01-18
gmungoc
JAL-3143 'id' not 'ID' attribute drives generation...
tree
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commitdiff
2018-12-19
Jim Procter
Merge branch 'features/JAL-1767pcaInProject' into bug...
tree
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commitdiff
2018-09-11
Jim Procter
Merge branch 'develop' into releases/Release_2_11_Branch
tree
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commitdiff
2018-09-06
Jim Procter
JAL-3105 reallocate quality and consensus annotation...
tree
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commitdiff
2018-08-30
Jim Procter
JAL-3092 make sure base pair counter is always moved...
tree
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commitdiff
2018-05-15
gmungoc
JAL-1264 exclude score-only from 'Add Reference Annotat...
tree
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commitdiff
2018-05-07
gmungoc
JAL-1767 unit test for save and restore PCA
features/JAL-1767pcaInProject
tree
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commitdiff
2018-05-07
gmungoc
JAL-1767 save PCA D and E vectors instead of 'details...
tree
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commitdiff
2018-05-04
gmungoc
JAL-1767 refactorings to enable faithful restore of...
tree
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commitdiff
2018-04-27
gmungoc
JAL-1767 refactoring and tidying of RotatableCanvas...
tree
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commitdiff
2018-04-26
gmungoc
JAL-2962 remove Change Parameters menu from PCA panel
tree
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commitdiff
2018-04-26
gmungoc
JAL-2962 code tidying/documentation (non-functional...
tree
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commitdiff
2018-04-25
gmungoc
JAL-1767 minor field tidying prior to functional changes
tree
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commitdiff
2018-04-16
gmungoc
JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe...
tree
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commitdiff
2018-03-30
gmungoc
JAL-2939 simplified way of getting hmm consensus residue
tree
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commitdiff
2018-03-26
gmungoc
JAL-2939 always store Information profile
tree
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commitdiff
2018-03-20
gmungoc
JAL-2629 InformationThread.findOrCreateAnnotation and...
tree
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commitdiff
2018-03-19
gmungoc
JAL-2620 parse genetic code tables from standard file...
tree
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commitdiff
2018-03-16
gmungoc
JAL-2620 alternative genetic code translation tables
tree
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commitdiff
2018-03-16
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2018-03-14
gmungoc
JAL-2933 pass viewport in Finder constructor, find...
bug/JAL-2839findWithHidden
tree
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commitdiff
2018-03-14
gmungoc
JAL-2933 gui and applet Finder hold a FinderI per viewport
tree
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commitdiff
2018-03-14
gmungoc
JAL-2839 refactored out getNextVisibleSequenceRegion
tree
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commitdiff
2018-03-13
gmungoc
JAL-2839 refactored analysis.Finder and tests
tree
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commitdiff
2018-03-09
gmungoc
JAL-2839 Finder refactoring prior to fixing the defect
tree
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commitdiff
2018-03-07
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-03-07
gmungoc
JAL-2629 storage and lifecycle of alignment/group HMM...
tree
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commitdiff
2018-02-28
gmungoc
JAL-2629 some tidying of Hmmer commands (wip)
tree
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commitdiff
2018-02-27
Jim Procter
Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104
tree
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commitdiff
2018-02-23
gmungoc
JAL-2599 parser and datamodel use primitive double...
tree
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commitdiff
2018-02-22
gmungoc
JAL-2629 tidy unit tests, constants etc
tree
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commitdiff
2018-02-20
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-02-09
gmungoc
JAL-2789 avoid using transcript (with no UTR) as CDS...
bug/JAL-2666
tree
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commitdiff
2018-02-09
gmungoc
JAL-2789 code format changes only (before functional...
tree
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commitdiff
2018-02-05
gmungoc
JAL-2897 more informative description on synonymous...
tree
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commitdiff
2018-02-05
gmungoc
Merge branch 'spikes/mungo' into trialMerge
tree
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commitdiff
2018-02-05
gmungoc
JAL-2897 more informative description on synonymous...
tree
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commitdiff
2018-01-30
gmungoc
JAL-1793 update spike build to latest incl stop and...
tree
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commitdiff
2018-01-30
gmungoc
JAL-2898 show 'stop_gained' variants on peptide sequences
tree
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commitdiff
2018-01-30
gmungoc
JAL-2897 generate peptide variants for synonymous codon...
tree
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commitdiff
2018-01-30
gmungoc
JAL-2897 formatting change only prior to functional...
tree
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commitdiff
2017-11-08
kiramt
Merge branch 'develop' into feature/JAL-2759
tree
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commitdiff
2017-10-27
gmungoc
JAL-1793 spike branch updated to latest
tree
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commitdiff
2017-10-27
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-10-26
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-10-26
Jim Procter
Merge branch 'features/JAL-2685pairwiseSeqLimits' into...
tree
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commitdiff
2017-10-05
gmungoc
JAL-2738 update spikes/mungo
tree
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commitdiff
2017-10-05
gmungoc
JAL-2755 transfer chromosomal reference from transcript...
tree
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commitdiff
2017-10-04
gmungoc
JAL-2738 match consequence "Allele" to VCF allele;...
tree
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commitdiff
2017-10-03
kiramt
JAL-2674 testing
tree
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commitdiff
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
tree
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commitdiff
2017-09-29
kiramt
JAL-2674 finish with iterators for now
tree
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commitdiff
2017-09-28
kiramt
JAL-2647 more iterators
tree
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commitdiff
2017-09-26
gmungoc
JAL-2738 JAL-2154 add DBRef from transcript to synthesi...
tree
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commitdiff
2017-09-25
gmungoc
JAL-2738 one constant in codebase for "alleles" attribu...
tree
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commitdiff
2017-09-21
gmungoc
JAL-2738 compute VCF on peptide, extract AF (allele...
tree
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commitdiff
2017-09-04
gmungoc
JAL-2617 unit tests for CDS + stop codon, CDS with...
bug/JAL-2617mappedStopCodon
tree
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commitdiff
2017-09-01
gmungoc
JAL-2617 omit stop codon from synthesized CDS sequence
tree
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commitdiff
2017-08-30
gmungoc
JAL-2685 tweaks to output spacing, updated TestAlignSeq...
tree
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commitdiff
2017-08-30
gmungoc
JAL-2685 use actual selection for report of pairwise...
tree
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commitdiff
2017-08-28
tzvanaalten
JAL-2629 add option to set HMM Logo letter height to...
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 hmm annotation consensus characters are now...
tree
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commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
tree
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commitdiff
2017-08-18
TZVanaalten
Merge branch 'develop' into features/hmmer
tree
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commitdiff
2017-08-18
TZVanaalten
JAL-2668 add tests for HMMER commands, annotation and io
tree
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commitdiff
2017-08-17
TZVanaalten
JAL-2629 add documentation to previous work
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 add GPL to main sources
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
tree
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commitdiff
2017-08-16
TZVanaalten
JAL-2599 HMM annotation now shows consensus characters...
tree
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commitdiff
2017-08-16
TZVanaalten
JAL-2599 fix background frequency storage and correct...
tree
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commitdiff
2017-08-10
TZVanaalten
JAL-2629 hmmalign now correctly creates a new frame
tree
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commitdiff
2017-08-02
TZVanaalten
JAL-2599 fix for HMM logo not normalising correctly
tree
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commitdiff
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